Question: Dictionary size problem in Picard CalculateHsMetrics
gravatar for nicola.licheri
2.6 years ago by
nicola.licheri0 wrote:

Hi everyone,

I'm following a Roche pipeline for the analysis of targeted bisulfite sequencing data and I'm in trouble with Picard CalculateHsMetrics.

I create the indexed reference file with samtools faidx command and the indexed .bam with samtools index.

When I run Picard, with the following command

java -Xmx4g -Xms4g -jar ~/bioTool/picard-tools-2.2.1/picard.jar CalculateHsMetrics BAIT_INTERVALS=DESIGN_bait_intervals.txt TARGET_INTERVALS=DESIGN_target_intervals.txt INPUT=2101435_S8_L001.clipped.bam.bai OUTPUT=2101435_S8_L001_picard_hs_metrics.txt METRIC_ACCUMULATION_LEVEL=ALL_READS REFERENCE_SEQUENCE=~/Data/MethylSeq/genomes/GRCh37_latest_genomic_idx.fa  VALIDATION_STRINGENCY=LENIENT TMP_DIR=.

it terminates with the following exception:

Exception in thread "main" htsjdk.samtools.util.SequenceUtil$SequenceListsDifferException: Sequence dictionaries are not the same size (0, 297)
    at htsjdk.samtools.util.SequenceUtil.assertSequenceListsEqual(
    at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(
    at htsjdk.samtools.util.SequenceUtil.assertSequenceDictionariesEqual(
    at picard.analysis.directed.CollectTargetedMetrics.doWork(
    at picard.cmdline.CommandLineProgram.instanceMain(
    at picard.cmdline.PicardCommandLine.instanceMain(
    at picard.cmdline.PicardCommandLine.main(

It seems like there is a problem in the indexes, but I cannot figure it out.

picard software error • 1.4k views
ADD COMMENTlink modified 2.6 years ago by Devon Ryan97k • written 2.6 years ago by nicola.licheri0
gravatar for finswimmer
2.6 years ago by
finswimmer14k wrote:

Hello nicola,

you are passing the bam index file (bam.bai) to picard. But this have to be the bam file itsself.

fin swimmer

ADD COMMENTlink modified 2.6 years ago • written 2.6 years ago by finswimmer14k

Awesome!! Thank you!

ADD REPLYlink written 2.6 years ago by nicola.licheri0

You're very welcome.

Please mark the answer as accepted if this solve your problem.

fin swimmer

ADD REPLYlink written 2.6 years ago by finswimmer14k
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